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minor patch to highlight quarto dependency
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sigven committed Aug 3, 2024
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3 changes: 1 addition & 2 deletions DESCRIPTION
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Expand Up @@ -17,8 +17,7 @@ Description: oncoEnrichR performs annotation and prioritization of genesets
patterns in human tumor samples), STRING/BioGRID (protein-protein interaction networks),
curated protein complexes (CORUM/Compleat/ComplexPortal/hu.MAP2),
COMPARTMENTS (subcellular compartments),
Human Protein Atlas (tissue and cell-type specific expression patterns and
prognostic associations), CellChatDB (ligand-receptor interactions),
Human Protein Atlas (prognostic gene expression associations), CellChatDB (ligand-receptor interactions),
DoRothEA (regulatory interactions), synthetic lethality predictions,
and Gene Ontology/MSigDB/REACTOME/KEGG/NetPath
(functional enrichment/over-representation analysis with respect to gene
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -20,7 +20,7 @@ Web-based access to **oncoEnrichR** is available at [**https://oncotools.elixir.

## News

- August 2nd 2024 [**1.5.0 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-5-0)
- August 3rd 2024 [**1.5.1 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-5-0)
- August 16th 2023: [**1.4.2 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-4-2)
- June 18th 2023: [**1.4.1 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-4-1)
- February 21st 2023 [**1.4.0 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-4-0)
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4 changes: 2 additions & 2 deletions data_processing_code/RELEASE_NOTES.txt
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@@ -1,6 +1,6 @@
##ONCOENRICHR_DB_VERSION = 20240801
##ONCOENRICHR_DB_VERSION = 20240803
name url description version key resource_type license
oncoEnrichR https://github.com/sigven/oncoEnrichR R package for functional interrogation of genesets in the context of cancer v1.5.0 oncoEnrichR software MIT
oncoEnrichR https://github.com/sigven/oncoEnrichR R package for functional interrogation of genesets in the context of cancer v1.5.1 oncoEnrichR software MIT
clusterProfiler https://guangchuangyu.github.io/software/clusterProfiler/ A universal enrichment tool for interpreting omics data (R package) v4.12.0 clusterProfiler software Artistic-2.0
OmnipathR https://omnipathdb.org/ Access to datasets on prior molecular knowledge: gene regulatory interactions, enzyme-PTM relationships, protein complexes, protein annotations etc. v3.11.10 omnipathr software MIT
hu.MAP http://humap2.proteincomplexes.org/ Human Protein Complex Map v2.0 humap2 db CC0 1.0
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2 changes: 1 addition & 1 deletion data_processing_code/data_raw.R
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Expand Up @@ -21,7 +21,7 @@ db_updates[['omnipath_regulatory']] <- F
db_updates[['subcelldb']] <- F
db_updates[['ligand_receptor_db']] <- F

oe_version <- "1.5.0"
oe_version <- "1.5.1"

data_raw_dir <-
"/Users/sigven/project_data/packages/package__oncoEnrichR/db/raw"
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6 changes: 3 additions & 3 deletions docker/Dockerfile
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Expand Up @@ -45,15 +45,15 @@ RUN cd cmake-3.20.0 && ./bootstrap && make && make install
## PINNED versions of all packages can be found in /renv.lock (JSON format)
RUN R -e "install.packages(repos = NULL, 'https://cloud.r-project.org/src/contrib/renv_1.0.7.tar.gz', lib = '/usr/lib/R/library/')"
COPY renv.lock /
COPY oncoEnrichR_1.5.0.tar.gz /
COPY oncoEnrichR_1.5.1.tar.gz /

#RUN R -e "library(renv)"

RUN R -e "library(renv); renv::restore(prompt = F, library = '/usr/lib/R/library/')"
WORKDIR /

## PINNED version - oncoEnrichR
RUN R -e "install.packages(repos = NULL, 'oncoEnrichR_1.5.0.tar.gz', lib = '/usr/lib/R/library/')"
RUN R -e "install.packages(repos = NULL, 'oncoEnrichR_1.5.1.tar.gz', lib = '/usr/lib/R/library/')"

## PINNED VERSION: pandoc (for HTML report generation)
RUN wget https://github.com/jgm/pandoc/releases/download/2.13/pandoc-2.13-1-amd64.deb && \
Expand All @@ -72,5 +72,5 @@ RUN gdebi --non-interactive quarto-linux-amd64.deb
RUN rm -f quarto-linux-amd64.deb

RUN rm -rf /root/.cache
RUN rm -rf /oncoEnrichR_1.5.0.tar.gz
RUN rm -rf /oncoEnrichR_1.5.1.tar.gz
RUN rm -rf /cmake-3.20.0*
2 changes: 1 addition & 1 deletion inst/templates/quarto/_documentation_workflow.qmd
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Expand Up @@ -6,7 +6,7 @@
::: {.callout-important}
## Citation policies for usage of report contents

We encourage users of _oncoEnrichR_ to properly cite no only the software but also the underlying data sources and other software tools used in the analysis. Below, we provide a guide as to the recommended citations for the various output modules of the report.
We encourage users of _oncoEnrichR_ to properly cite not only the software, but also the underlying data sources and other software tools used in the analysis. Below, we provide a guide as to the underlying citations for the various output modules of the report.
:::

:::: {.columns}
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17 changes: 17 additions & 0 deletions pkgdown/_pkgdown.yml
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Expand Up @@ -4,6 +4,17 @@ toc:
depth: 3
template:
bootstrap: 5
bslib:
info: "#014587"
dropdown-link-hover-bg: "#014587"
dropdown-link-hover-color: "white"
dropdown-link-active-color: "white"
navbar-light-color: "white"
navbar-light-brand-color: "white"
navbar-link-hover-color: "white !important"
nav-link-hover-color: "white !important"
navbar-light-brand-hover-color: "white !important"
navbar-link-color: "white"
includes:
in_header: |
<script async src="https://www.googletagmanager.com/gtag/js?id=G-N4MB4571K5"></script>
Expand All @@ -18,6 +29,12 @@ authors:
Sigve Nakken:
href: "https://github.com/sigven"
navbar:
link-color: "white"
light-color: "white"
light-brand-color: "white"
light-hover-color: "white !important"
type: light
bg: info
structure:
left: [home, installation, running, articles, changelog]
right: [reference, search, github]
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2 changes: 1 addition & 1 deletion pkgdown/index.md
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Expand Up @@ -85,7 +85,7 @@ See also the [output views](articles/output.html) that addresses each of the que

## News

- August 2nd 2024: [**1.5.0 release**](articles/CHANGELOG.html#version-1-5-0)
- August 3rd 2024: [**1.5.1 release**](articles/CHANGELOG.html#version-1-5-1)
- August 16th 2023: [**1.4.2 release**](articles/CHANGELOG.html#version-1-4-2)
- June 18th 2023: [**1.4.1 release**](articles/CHANGELOG.html#version-1-4-1)
- February 21st 2023: [**1.4.0 release**](articles/CHANGELOG.html#version-1-4-0)
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7 changes: 7 additions & 0 deletions vignettes/CHANGELOG.Rmd
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Expand Up @@ -7,6 +7,13 @@ vignette: >
%\usepackage[UTF-8]{inputenc}
---

## Version 1.5.1

* Date: 2024-08-03

* Updates
* Minor patch that highlights `quarto` as package dependency in installation instructions

## Version 1.5.0

* Date: 2024-08-02
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6 changes: 5 additions & 1 deletion vignettes/installation.Rmd
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Expand Up @@ -9,7 +9,11 @@ vignette: >

## Requirements/dependencies

* _oncoEnrichR_ requires R (>= version 4.1)
* R (>= version 4.1)
* **quarto CLI**
- Downloads available for different platforms here: [https://github.com/quarto-dev/quarto-cli/releases](https://github.com/quarto-dev/quarto-cli/releases)
- When installing on Linux, make sure you include `quarto` in your PATH variable, see instructions [here](https://quarto.org/docs/download/tarball.html)
- Ensure that quarto is correctly installed through `quarto check`

## Installation of oncoEnrichR with R commands

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